AlphaFold Colab ValueError Step 5

[theflyelectric]

Can someone explain why this error occurred? I would also like to know how to fix it. Should I just with run_relax turned off? Thanks, Nigel

AMBER relaxation: 86% 6/7 [elapsed: 30:40 remaining: 04:45] /usr/local/lib/python3.7/dist-packages/jax/_src/tree_util.py:189: FutureWarning: jax.tree_util.tree_multimap() is deprecated. Please use jax.tree_util.tree_map() instead as a drop-in replacement. 'instead as a drop-in replacement.', FutureWarning)

ValueError Traceback (most recent call last) in () 88 max_outer_iterations=3, 89 use_gpu=True) ---> 90 relaxed_pdb, _, _ = amber_relaxer.process(prot=unrelaxed_proteins[best_model_name]) 91 else: 92 print('Warning: Running without the relaxation stage.')

2 frames /opt/conda/lib/python3.7/site-packages/alphafold/relax/amber_minimize.py in _run_one_iteration(pdb_string, max_iterations, tolerance, stiffness, restraint_set, max_attempts, use_gpu, exclude_residues) 417 logging.info(e) 418 if not minimized: --> 419 raise ValueError(f"Minimization failed after {max_attempts} attempts.") 420 ret["opt_time"] = time.time() - start 421 ret["min_attempts"] = attempts

ValueError: Minimization failed after 100 attempts.

[CameronWeller]

having the same issue. looks like some dependency is out of date. Kinda have to just wait for the devs to fix it it seems. Or, hopefully someone posts a workaround.

[Htomlinson14]

Thanks for raising this issue! Closing as this duplicates https://github.com/deepmind/alphafold/issues/383